I don't know if this has been thought of, since I was locked away for many months, but...
I think at the play call screen, when you scroll through your formations, you should be able to scroll through each player on the field with your right analog stick by pushing left and right, then when you get on the player you want to sub out, then push up and down with the right analog stick and that will sub in any player on the bench (starting with the most qualified player, and scrolling down to the least). For example....at the play call screen, I pick singleback 2 TE 2 WR. Wtih the right stick, I push left and scroll through each player in that formation. Until I get to, let's say, the 2nd TE. Perhaps the 2nd TE is a better blocker, and you want a better recieving TE. So you then push up and down on the right stick, and it subs in the next best qualified player for that position, which would be the 3rd TE, then probably the 3rd WR, then the 4th WR, and so on. You could even put a tackle there or a guard to boost the blocking if you needed. I think this would be so much better than the circle button option, which gives you only a few substition options. With my idea, you have virtually unlimited options.
Thanks, and sorry if I posted something thats already been thought of.